# This file is the result of combining several RDB files, specifically # T0272.t04.dssp-ebghstl.rdb (weight 1.53986) # T0272.t04.stride-ebghtl.rdb (weight 1.24869) # T0272.t04.str2.rdb (weight 1.54758) # T0272.t04.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0272.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0272 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0272.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0272.t04.stride-ebghtl.rdb # ============================================ # TARGET T0272 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0272.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0272.t04.str2.rdb # ============================================ # TARGET T0272 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0272.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ # Comments from T0272.t04.alpha.rdb # ============================================ # TARGET T0272 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0272.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4176 0.0339 0.5485 2 W 0.7394 0.0240 0.2366 3 L 0.7787 0.0254 0.1959 4 T 0.7226 0.0562 0.2212 5 K 0.7583 0.0374 0.2043 6 L 0.7746 0.0276 0.1978 7 V 0.6261 0.0223 0.3516 8 L 0.3533 0.0228 0.6239 9 N 0.1328 0.0126 0.8546 10 P 0.0114 0.4802 0.5084 11 A 0.0156 0.4715 0.5129 12 S 0.0473 0.5797 0.3730 13 R 0.0083 0.8689 0.1228 14 A 0.0110 0.8582 0.1308 15 A 0.0143 0.8433 0.1424 16 R 0.0158 0.8231 0.1611 17 R 0.0236 0.7487 0.2277 18 D 0.0283 0.6150 0.3567 19 L 0.0326 0.4749 0.4925 20 A 0.0551 0.2317 0.7132 21 N 0.0872 0.0561 0.8566 22 P 0.0071 0.8054 0.1875 23 Y 0.0062 0.8274 0.1664 24 E 0.0083 0.8495 0.1421 25 M 0.0122 0.8217 0.1660 26 H 0.0127 0.7960 0.1913 27 R 0.0079 0.8519 0.1402 28 T 0.0117 0.8424 0.1459 29 L 0.0137 0.8581 0.1283 30 S 0.0136 0.8665 0.1200 31 K 0.0103 0.9001 0.0896 32 A 0.0162 0.8937 0.0901 33 V 0.0219 0.8825 0.0955 34 S 0.0241 0.8497 0.1262 35 R 0.0212 0.7800 0.1988 36 A 0.0241 0.7002 0.2756 37 L 0.0277 0.6241 0.3483 38 E 0.0215 0.6382 0.3403 39 E 0.0323 0.5311 0.4366 40 G 0.0324 0.4854 0.4823 41 R 0.0389 0.5008 0.4603 42 E 0.0648 0.4964 0.4389 43 R 0.1327 0.4119 0.4554 44 L 0.3264 0.3430 0.3306 45 L 0.4668 0.2815 0.2517 46 W 0.5138 0.2632 0.2230 47 R 0.4998 0.2263 0.2739 48 L 0.4172 0.1130 0.4698 49 E 0.2226 0.0614 0.7160 50 P 0.1113 0.0738 0.8150 51 A 0.0678 0.1355 0.7967 52 R 0.0542 0.1802 0.7657 53 G 0.0451 0.1456 0.8093 54 L 0.0970 0.0611 0.8419 55 E 0.0846 0.0359 0.8796 56 P 0.0914 0.0258 0.8828 57 P 0.2322 0.0252 0.7426 58 V 0.7982 0.0085 0.1933 59 V 0.9215 0.0041 0.0744 60 L 0.9286 0.0045 0.0668 61 V 0.9157 0.0054 0.0789 62 Q 0.8237 0.0090 0.1673 63 T 0.4832 0.0154 0.5013 64 L 0.1738 0.0521 0.7741 65 T 0.1254 0.0558 0.8188 66 E 0.0682 0.0881 0.8437 67 P 0.0585 0.1659 0.7756 68 D 0.1002 0.2040 0.6957 69 W 0.0592 0.5614 0.3795 70 S 0.1048 0.5155 0.3798 71 V 0.2001 0.4601 0.3399 72 L 0.1817 0.2025 0.6158 73 D 0.1036 0.1814 0.7151 74 E 0.0384 0.2336 0.7280 75 G 0.0706 0.1653 0.7641 76 Y 0.3228 0.1621 0.5151 77 A 0.4897 0.1254 0.3849 78 Q 0.5252 0.1065 0.3682 79 V 0.5295 0.0707 0.3998 80 F 0.2618 0.0292 0.7090 81 P 0.0977 0.0226 0.8798 82 P 0.0711 0.0599 0.8690 83 K 0.0742 0.0848 0.8410 84 P 0.0554 0.2780 0.6666 85 F 0.0691 0.3111 0.6199 86 H 0.0811 0.3175 0.6015 87 P 0.0191 0.5383 0.4426 88 A 0.0359 0.4692 0.4949 89 L 0.1090 0.1607 0.7303 90 K 0.0565 0.0350 0.9084 91 P 0.0229 0.1212 0.8560 92 G 0.0398 0.0686 0.8916 93 Q 0.3154 0.0441 0.6406 94 R 0.6922 0.0187 0.2891 95 L 0.8629 0.0114 0.1258 96 R 0.8755 0.0155 0.1090 97 F 0.8807 0.0136 0.1057 98 R 0.8518 0.0213 0.1269 99 L 0.8033 0.0280 0.1687 100 R 0.6334 0.0399 0.3267 101 A 0.3803 0.0449 0.5748 102 N 0.1578 0.0297 0.8125 103 P 0.0387 0.4950 0.4663 104 A 0.0590 0.5025 0.4385 105 K 0.0906 0.5107 0.3987 106 R 0.1377 0.5023 0.3600 107 L 0.1332 0.5058 0.3610 108 A 0.1267 0.3972 0.4761 109 A 0.1684 0.2982 0.5334 110 T 0.1209 0.1805 0.6986 111 G 0.0597 0.0471 0.8932